sampleMetagenomeResults

Output of `ProActiveDetect()`
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internal

Automate the detection of gaps and elevations in mapped sequencing
read coverage using a 2D pattern-matching algorithm. 'ProActive' detects, characterizes
and visualizes read coverage patterns in both genomes and metagenomes. Optionally,
users may provide gene annotations associated with their genome or metagenome
in the form of a .gff file. In this case, 'ProActive' will generate an additional
output table containing the gene annotations found within the detected regions of gapped
and elevated read coverage. Additionally, users can search for gene
annotations of interest in the output read coverage plots.

Jessie Maier

ProActive

Detect Elevations and Gaps in Mapped Sequencing Read Coverage

Manuel Kleiner

sampleMetagenomeResults function

## `sampleMetagenomeResults`
A list with 6 objects:<dl>
 <dt>SummaryTable</dt>
<dd>A table containing all pattern-matching classifications</dd> <dt>CleanSummaryTable</dt>
<dd>A table containing only gap and elevation pattern-match
classifications (i.e. noPattern classifications removed)</dd> <dt>PatternMatches</dt>
<dd>A list object containing information needed to visualize the
pattern-matches in `plotProActiveResults()`</dd> <dt>FilteredOut</dt>
<dd>A table containing contigs/chunks that were filtered out for being
too small or having too low read coverage</dd> <dt>Arguments</dt>
<dd>A list object containing arguments used for pattern-matching (windowSize,
mode, chunkSize, chunkContigs)</dd> <dt>GeneAnnotTable</dt>
<dd>A table containing gene predictions associated with elevated
or gapped regions in pattern-matches</dd>
</dl>

Format

sampleMetagenomeResults — sampleMetagenomeResults

## `sampleMetagenomeResults`
A list with 6 objects:<dl>
 <dt>SummaryTable</dt>
<dd>A table containing all pattern-matching classifications</dd>

 <dt>CleanSummaryTable</dt>
<dd>A table containing only gap and elevation pattern-match
classifications (i.e. noPattern classifications removed)</dd>

 <dt>PatternMatches</dt>
<dd>A list object containing information needed to visualize the
pattern-matches in `plotProActiveResults()`</dd>

 <dt>FilteredOut</dt>
<dd>A table containing contigs/chunks that were filtered out for being
too small or having too low read coverage</dd>

 <dt>Arguments</dt>
<dd>A list object containing arguments used for pattern-matching (windowSize,
mode, chunkSize, chunkContigs)</dd>

 <dt>GeneAnnotTable</dt>
<dd>A table containing gene predictions associated with elevated
or gapped regions in pattern-matches</dd>


</dl>

sampleMetagenomeResults: sampleMetagenomeResults

Description

Usage

Arguments

Format

Details